"I have two small embryos preserved in alcohol, that I forgot to label. At present I am unable to determine the genus to which they belong. They may be lizards, small birds, or even mammals."

The changes undergone by a developing embryo forms an hourglass: early on embryos from different species vary significantly, later on they converge to be similar, and finally they diverge again, to develop into very different animals. This middle stage - the phylotypic stage - is when different animals from different threads of life, whether they be zebrafish or mice or chicken all resemble each other.

Why?

Von Baer was a Christian believer, and saw the handiwork of god implicit in the similarities. The elegance of having different species appear similar before sprouting variations suggested a proto-plan to which each animal abided before going its own way. The nineteenth century scientist was right to see a single plan maintained across the various species, but his explanation was too simple.

In late 2010 the science journal Nature published two studies that addressed this problem, here's what they found:

Samples were taken from embryos at different time points and measured using microarray technology: the expressed genes from the sample were copied, labeled, and washed over a microarray containing a pattern of DNA fragments. The microarray was scanned for the label, and computed, providing an output of which genes were expressed.

Once they had measured gene expression over time for a single species, it was easy to repeat the procedure for the other species.

With this data the group could ask: how doe the difference in gene expression between species change as the animals' develop? And the answer: Gene expression is very different at the beginning and end of embryo development, but is most similar in the middle. The group also showed that the genes that best conformed to this hourglass model were genes known to be involved in embryo development. Thus they could conclude the phylotypic stage of development could be defined, not just on the basis of morphology, but also on the basis of developmental genes' expression.

Whereas the above study compared gene expression across species, this study looked at gene expression in a single animal.

This group had previously developed a technique called phylostratigraphy (phylum + stratigraphy). This is a bioinfomatic technique that analyzes the contents of a DNA, and attributes ages to the genes. It achieves this by determining when a particular gene arose on the basis of which forms of life have it, and which don't. If, for example, a gene is present in a mouse and a human, it means that the gene was likely present in the common ancestor of mice and humans. If the gene only appears in one of mice or humans, then it likely arose after the two lineages diverged.

Here too, the group took samples at different stages of embryonic development, then submitted the samples to analysis using microarrays. This output told them which genes were activated at different stages of development. They then submitted this data to their phylostraitographic algorithm.

The output of this was to tell them the evolutionary age of the genes expressed, and how this changes as the animal develops. Here too they found an hourglass pattern: The genes at early and late stages are the most recent, whereas those in the middle are the oldest. In other words, during the phylotypic stage of development, organisms tend towards using their older genes.

What does it all mean?

To restate, the two papers showed that, as compared to other stages, the genes expressed during the phylotypic stage:

Display higher similarity between species

Display older ancestry

This provides a genetic and evolutionary basis for the morphological similarities observed by old Karl von Baer, but it also reinforces another old question: why? There are two viable and popular, and somewhat overlapping, hypotheses that could explain this phenomenon. Both hypotheses assume that there is some feature which is so necessary to development that it is resistant to evolutionary change.

The first hypothesis predicts that the feature that is resistant to change in the phylotypic stage is the interconnectedness of the signaling networks. The second hypothesis predicts that the resistant feature is the connection between growth and patterning, as evidenced by the primordial Hox genes.

The first hypothesis interprets the phylotypic stage as being the last time in development when everything depends on everything else. Later development is significantly modular, so that for example each limb develops with reference to itself, and the effect of mutations may be limited to affecting discrete pathways. By depending on an increased level of pathway interconnectivity, the phylotypic stage tests and ensures the viability of the entire network.

The second hypothesis interprets the phylotypic stage as being the informational cornerstone of development. The formation of complex lifeforms depend on the construction of a form-neutral skeletal pattern, onto which specific instructions for form may be interpreted. This requirement for a base code onto which any and all instructions can be linked is provided during the phylotypic stage.